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Create a map of bioregions

Source: R/map_bioregions.R
map_bioregions.Rd

This plot function can be used to visualize bioregions based on a bioregion.clusters object combined with a spatial object (sf or terra).

Usage

map_bioregions(
  bioregionalization,
  map,
  partition_index = NULL,
  map_as_output = FALSE,
  plot = TRUE,
  clusters = NULL,
  geometry = NULL,
  write_clusters = NULL,
  ...
)

Arguments

bioregionalization

A bioregion.clusters object.

map

A spatial object that can be handled by sf or terra. The first attribute or layer should correspond to the sites' ID (see Details).

partition_index

An integer, character, or NULL specifying which bioregionalization's partition(s) to plot. By default (NULL), all partitions are plotted. If an integer or vector of integers is provided, partition(s) are selected by column number(s) in the bioregionalization data.frame (starting from 1 after the ID column). If a character or vector of characters, partition(s) are selected by name(s) matching column names in bioregionalization.

map_as_output

A boolean indicating if the sf data.frame object used for the plot should be returned.

plot

A boolean indicating if the plot should be drawn.

clusters

Deprecated. Use bioregionalization instead. The former bioregionalization has been replaced by partition_index.

geometry

Deprecated. Use map instead.

write_clusters

Deprecated. Use map_as_output instead.

...

Further arguments to be passed to sf::plot().

Value

One or several maps of bioregions if plot = TRUE and the sf data.frame object used for the plot if map_as_output = TRUE.

Details

The site IDs in bioregionalization and map should correspond. They must have the same type (i.e., character if bioregionalization is a bioregion.clusters object), and the sites in bioregionalization should be included among the sites in map. If map is an sf or a SpatVector (terra) object, it should contain an attribute table with the IDs in the first column. If map is a SpatRaster (terra) object, it should contain the IDs in the first layer.

If the bioregionalization object contains both types of nodes (sites and species), only site will be mapped. The function automatically filters to site nodes using the node_type attribute.

Colors: If the bioregionalization object contains colors (added via bioregion_colors()), these colors will be automatically used for plotting. Otherwise, the default sf color scheme will be applied.

See also

For more details illustrated with a practical example, see the vignette: https://biorgeo.github.io/bioregion/articles/a5_1_visualization.html.

Associated functions: bioregion_colors

Author

Maxime Lenormand (maxime.lenormand@inrae.fr)
Boris Leroy (leroy.boris@gmail.com)
Pierre Denelle (pierre.denelle@gmail.com)

Examples

data(fishmat)
data(fishsf)

net <- similarity(fishmat, metric = "Simpson")
clu <- netclu_greedy(net)
mapclu <- map_bioregions(clu, 
                         map = fishsf, 
                         map_as_output = TRUE, 
                         plot = FALSE)

# With colors
clu_colored <- bioregion_colors(clu)
mapclu <- map_bioregions(clu_colored, 
                         map = fishsf, 
                         map_as_output = TRUE, 
                         plot = FALSE)